4. Analyze Your Methylome Data Using RnBeads

Example Reports

Epigenomics 2016

This tutorial contains instructions and material for the workshop on "Analyzing Methylome Data using RnBeads" that was presented at the Epigenomics 2016 meeting.
To get R and RnBeads set up for the tutorial and to retrieve the example data, please follow steps 1, 2 and 3 described below. Afterwards, feel free to experiment with the code contained in the downloaded data directory.

4. Analyze Your Methylome Data Using RnBeads

Example Reports

Age Prediction Using RnBeads

Here, we provide instructions for how to use the epigenetic age prediction tool MethylAger. MethylAger was created as an RnBeads module and is therefore applicable to all DNA methylation assays operating at single base pair resolution. MethylAger contains several predefined predictors that were extensively evaluated for the most frequently used DNA methylation assays (e.g. 27K, 450K and RRBS). Depending on the type of the input data set, MethylAger decides which of these predictors is applicable. Additionally, a custom predictor can be created from the provided data set. For a detailed description of the methods employed and of the predefined predictors explore this website. Similar to the tutorial described above, an installation of R is needed. Then follow the instructions and enjoy the functions of the epigenetic age prediction tool MethylAger.

1. Download R Tutorial and Data Set

The data package, including the R tutorial and an example data set can be downloaded here (233 MB).

2. Use MethylAger

Follow the instructions provided in the R tutorial and analyze the example data set to get used to MethylAger.

Additional Information

Cross-platform analysis with RnBeads

This tutorial is a brief demo of the new functionality for the joint storage and analysis of data from different DNA methylation profiling platforms. The updated combine method enables pair-wise merging of all classes of data containers. Obtained hybrid data sets can be used for any standard RnBeads analysis. The tutorial demonstrates new functionality using pubicly available data of primary prostate cancer samples and cell lines from the EPIC array evaluation study [Pidsley et al., Genome Biology, 2016]

Support for Additional Genome Assemblies

RnBeads relies on annotation packages – one for every supported genome assembly. The ones currently supported are hg19, hg38, mm9, mm10 and rn5. If you would like to analyze a different genome, you need to create a new annotation package. RnBeadsAnnotationCreator facilitates the generation of annotation packages for RnBeads.

A dedicated vignette (download PDF) explains how RnBeads annotation packages are structured and includes a tutorial on creating an annotation package for the Zebrafish genome.